Re: Re: look for substrings and getting their location


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Re: Re: look for substrings and getting their location

by biosysadmin (Deacon)

on May 09, 2004 at 17:47 UTC ( [id://351878]=note: print w/replies, xml )

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in reply to Re: look for substrings and getting their location
in thread look for substrings and getting their location

Excellent explanation of three functions that anyone doing biological research in Perl should know. :)

You should also check out using the BioPerl modules for doing your sequence input and output, it will make your program general enough to work with many different sequence formats, not just FASTA. Here's a quick example:

use Bio::SeqIO;

my $filename = 'test.seq';
my $format = 'fasta';

my $seqio = Bio::SeqIO->new( -file => $filename, -format => $format );
while ( my $seqobj = $seqio->next_seq() ) {
   my $raw_sequence = $seqobj->seq;
   # do your searching on this raw sequence
}
[download]

Hope this helps. :)